Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1751 to 1800 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
876 5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131] Divided 212.002 203.954 1.03946
tax interaction protein 1. [refseq;acc:nm_014604] Subtracted 223.906 215.653 8.253
877 5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741] Divided 212.002 203.954 1.03946
zinc finger protein 444; endothelial zinc finger protein 2. [refseq;acc:nm_018337] Subtracted 269.896 278.093 8.197
878 5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9] Divided 212.002 203.954 1.03946
syntaxin 7. [swissprot;acc:o15400] Subtracted 217.181 209.012 8.169
879 5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478] Divided 212.002 203.954 1.03946
phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [swissprot;acc:q9y285] Subtracted 217.491 209.323 8.168
880 5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0] Divided 212.002 203.954 1.03946
phenylalanine-trna synthetase. [refseq;acc:nm_006567] Subtracted 217.491 209.323 8.168
881 l-myc-1 proto-oncogene protein. [swissprot;acc:p12524] Divided 227.604 219.001 1.03928
transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290] Subtracted 211.961 203.814 8.147
882 mitochondrial import receptor subunit tom20 homolog (mitochondrial 20 kda outer membrane protein) (outer mitochondrial membrane receptor tom20). [swissprot;acc:q15388] 198.781 190.66 8.121
n-myc proto-oncogene protein. [swissprot;acc:p04198] Divided 227.601 219.008 1.03924
883 ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546] 227.596 219.017 1.03917
peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [swissprot;acc:p40855] Subtracted 198.781 190.66 8.121
884 ga binding protein beta-2 chain (gabp-beta-2 subunit) (transcription factor e4tf1-47) (gapbp-2) (nuclear respiratory factor-2 subunit gamma). [swissprot;acc:q06545] Divided 227.596 219.017 1.03917
sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [refseq;acc:nm_016538] Subtracted 232.473 224.372 8.101
885 casein kinase ii beta chain (ck ii) (phosvitin) (g5a). [swissprot;acc:p13862]
nadh-ubiquinone oxidoreductase 23 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-23kd) (ci-23kd) (tyky subunit). [swissprot;acc:o00217] Divided 227.596 219.017 1.03917
886 elongation of very long chain fatty acids protein 1 (cgi-88). [swissprot;acc:q9bw60] 219.018
transcription factor btf3 homolog 3. [swissprot;acc:q13892] Subtracted 211.908 203.832 8.076
887 5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619] 212.002 203.954 8.048
transducin beta-like 3; wd-repeat protein sazd. [refseq;acc:nm_006453] Divided 244.155 234.96 1.03913
888 5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646] Subtracted 212.002 203.954 8.048
nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594] Divided 212.027 204.05 1.03909
889 5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131] Subtracted 212.002 203.954 8.048
alpha-nac protein. [sptrembl;acc:q9h009] Divided 212.028 204.053 1.03908
890 5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741] Subtracted 212.002 203.954 8.048
syntaxin 7. [swissprot;acc:o15400] Divided 217.181 209.012 1.03908
891 5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9] Subtracted 212.002 203.954 8.048
small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173] Divided 212.028 204.055 1.03907
892 5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478] Subtracted 212.002 203.954 8.048
di-ras2. [refseq;acc:nm_017594] Divided 212.028 204.055 1.03907
893 5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0] Subtracted 212.002 203.954 8.048
myc proto-oncogene protein (c-myc). [swissprot;acc:p01106] Divided 227.585 219.037 1.03903
894 mitochondrial 60s ribosomal protein l27 (l27mt) (hspc250). [swissprot;acc:q9p0m9] Subtracted 231.163 239.205 8.042
phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [swissprot;acc:q9y285] Divided 217.491 209.323 1.03902
895 acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] Subtracted 164 155.961 8.039
phenylalanine-trna synthetase. [refseq;acc:nm_006567] Divided 217.491 209.323 1.03902
896 dna-directed rna polymerase ii 13.3 kda polypeptide (ec 2.7.7.6) (rpb11). [swissprot;acc:p52435] 230.811 239.785 1.03888
t-cell activation wd repeat protein. [refseq;acc:nm_139281] Subtracted 243.34 235.322 8.018
897 3-phosphoinositide dependent protein kinase-1 (ec 2.7.1.37) (hpdk1). [swissprot;acc:o15530] Divided 272.878 283.472 1.03882
prip-interacting protein pipmt; prip-interacting protein with methyltransferase domain. [refseq;acc:nm_024831] Subtracted 210.863 218.878 8.015
898 60s acidic ribosomal protein p1. [swissprot;acc:p05386] Divided 229.171 238.048 1.03874
pdz/coiled-coil domain binding partner for the rho-family gtpase tc10; fused in glioblastoma; golgi associated pdz and coiled-coil motif containing protein; cftr-associated ligand. [refseq;acc:nm_020399] Subtracted 210.863 218.878 8.015
899 nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594] 212.027 204.05 7.977
thioredoxin domain-containing 2; sperm-specific thioredoxin; thioredoxin domain-containing 2 (spermatozoa). [refseq;acc:nm_032243] Divided 229.171 238.048 1.03874
900 alpha-nac protein. [sptrembl;acc:q9h009] Subtracted 212.028 204.053 7.975
thioredoxin (atl-derived factor) (adf) (surface associated sulphydryl protein) (sasp). [swissprot;acc:p10599] Divided 229.171 238.048 1.03874

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.
- http://analysis.yellowcouch.org/